Dissertation

The Use of Genomic Epidemiology in Viral Outbreak Monitoring and Intervention

Matteson, Nathaniel L

2023

Overview

Viral infectious diseases are one of the greatest challenges public health faces. Since the beginning of the 21st century, a number of viruses have emerged which have not previously been encountered, such SARS and MERS coronaviruses, or have reappeared in new and naive locations, such as influenza, Ebola, West Nile, and Zika viruses. These outbreaks exact tolls on human health, regional security, and have the potential to spiral into global crises. Mitigating the effect of emerging diseases requires an understanding of the origin, magnitude, and location of virus transmission. Traditional epidemiological approaches that track the spread of the virus and quantify the effectiveness of interventions are labor-intensive and rely on interview-based contact tracing. As a result, these methods can simply not cope with the potentially massive amount of outbreak cases.Advances in virus sequencing and phylogenetics have transformed our ability to map the spread of viruses. So-called ”genomic epidemiology” approaches are capable of providing more insight into epidemiological dynamics than traditional approaches as they allow insights into the periods in which cases were unobserved. In this thesis, we apply genomic epidemiology to elucidate the transmission during two ongoing viral outbreaks: the COVID-19 pandemic, and West Nile virus in the Americas. By monitoring the spread of these viral threats in near real-time, we define transmission networks, provide mechanistic insights into the drivers of epidemic spread, and measure the impact of control measures. Ultimately, this work shows that coordination between genomic surveillance and public health can inform targeted control measures that effectively reduce viral disease risk.

• Publisher: ProQuest Dissertations & Theses
• Subject: Chemical engineering / Epidemiology / Genetics
• ISBN: 9798380376372